Alright, this is good, you're making me think deeply about this, and I appreciate it. Let's get into the qualities of moral acts some more.
To put more precisely part of what's already been discussed, there are three parts to a moral act: the object, the circumstances, and the end. The object is the thing acted upon, the end is the reason for which the act is done, and the circumstances are the conditions of the action, such as place, time, and so on. The object and end determine typically determine the moral quality of the act, but circumstances can, at times, modify that.
To apply that precisely in the case of the beggar, the end of giving the beggar cigarettes may be good or bad, depending on the giver's intentions. The object of the act, that is, giving the beggar cigarettes, is bad because cigarettes are harmful to the beggar's health. Therefore, that action is bad.
To apply this precision to the case of a soldier in a war, the objects and ends can be all over the place. Let's suppose the end, or intent, on the soldier's part is to defend his country. This is a good end. Let's take as an object firing a gun at an enemy. That is a bad object, however, in a particular circumstance, the soldier may be firing the gun at an enemy because it is the only means of achieving the end of defending his country. In this case, the extremity of the circumstances make the action morally good, if resulting in an unfortunate natural evil. The key here is extreme circumstances are required to make such an act morally good.
Extrapolating out to the scale of, say, a whole war, I think it is understandable that we typically give soldiers a pass, but that doesn't mean we necessarily should. However, greater responsibility lies in the leaders who order their soldiers into battle, to conduct a just war, that is, one oriented towards defense against an unjust aggressor, conducted as a last resort, and using the minimum violence necessary to repel the unjust aggression.
Zooming out again, the commandment is "thou shalt not kill." Killing as a moral act consists of a specific object, end, and circumstance. In the case of home defense or a just war, the type of moral act is defense, rather than killing. It's a very fine distinction, and thus the use of violence, even when it seems justified, always treads a very thin line, morally speaking. That's why violence should be avoided whenever possible.
I know I retreaded a bunch of ground, but I think it was good for the discussion and for my own understanding to put all this as precisely as possible. I hope I addressed some of your big-picture questions as well, from your last paragraph.
